Re: [AMBER-Developers] Third (final?) release candidate for Amber 12

From: <>
Date: Mon, 2 Apr 2012 05:03:02 -0400 (EDT)


>> > tail fecp2.pm6.sp.out
>> QMMM: System specified with odd number of electrons ( 57)
>> QMMM: but odd spin ( 1). You most likely have the charge of
>> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
>> calculation.
>> then test AT parallel: 37 passed, 0 fail
> weird....can you post the entire output file? This one has not been
> reported
> before (should find 58 electrons).

The output only contained this error. But I found that the input file does not have a newline after the last atom, apparently
this last hydrogen is not found then and an odd electron number is
obtained. Adding a newline at the end fixes this and the test passes.
Maybe my sqm compile is more strict about newlines?

>> and in qmmm_EXTERN/QMMM_MD_GAUSSIAN the scripts
>> ./Run.aladip.hf_sto-3g
>> ./Run.nma-spcfw-15.hf_sto-3g
>> fail because there is no g09 executable. I have g03 but not g09
>> installed,
>> I'm not sure why it fails instead of skipping the test.
> Is g03 in your path? Is g03 in $GAUSS_EXEDIR? If you unset your
> environment
> variable GAUSS_EXEDIR, it should skip the tests. On the other hand, it
> should
> work with either g03 or g09. Look at $AMBERHOME/test/check_GAUSSIAN.x.

g03 is in my PATH and in GAUSS_EXEDIR, therefore check_GAUSSIAN.x returns 0.
 But the test still tries to call g09 (which does not exist) and I could
not figure out where in e.g.


the actual name of the Gaussian executable is set. It looks like it checks
for g03 or g09, but then assumes g09 is installed.

>> also in qmmm_EXTERN/QMMM_MD_Orca ./Run.aladip.hf_sto-3g.MechEm fails and
>> in qmmm_EXTERN/QMMM_MD_TeraChem ./Run.aladip.hf_sto-3g.MechEm and
>> ./Run.nma-spcfw-15.hf_sto-3g.MechEm fail, all three by virtue of not
>> existing.
> Can you try to see why the check_Orca.x script is not correctly
> identifying
> that you don't have ORCA installed?

The check script is fine (I dont have Orca), but it isn't even called,
because the test files




do not exist. To me this looks like a test that has been removed but is
still called in the Makefile, or some files are missing in my tarball.

>> Furthermore in amoeba_wat2 test ./Run.ntpverlet.pmemd segfaulted with no
>> output but the 'Amber 11 SANDER...' output file header. huh?
> This is known behavior: pmemd.amoeba will fail badly if there is not
> enough
> stack space, but Bob never figured out how to correctly test for this. At
> least the error tells you not to run pmemd.amoeba....We should probably
> add
> a better explanation to the test script.

I reran this one with 400MB stack space and it still segfaulted. If that
is expected, then ok, I guess...


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Mon Apr 02 2012 - 02:30:04 PDT
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